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Introduction

Please see the WestGrid GROMACS page for some general remarks about running GROMACS on WestGrid systems. Specific scripts for running on Glacier are shown below. Scripts and data for sample runs are available on Glacier under /global/software/gromacs-3.3/job_examples. The scripts shown below are based on the bash shell, but, a C shell example is included in the job_examples directory.

In the combined example shown below, calls to grompp and mdrun are combined into a single job. In subsequent sections, scripts are shown to run grompp and mdrun separately. A script to run tpbconv, to process output from one mdrun job to prepare for a subsequent run, is also provided. However one of the simplest ways of submitting GROMACS jobs is to use a master script to run an alternating sequence of mdrun and tpbconv commands as discussed below.

Chaining GROMACS jobs

One of the simplest ways to submit GROMACS jobs on Glacier is to use the chain_glacier script. To try this, copy all the files from /global/software/gromacs-3.3/job_examples/chain into your own directory and execute:

Example combining grompp and mdrun in one job

Since the grompp preprocessor must be run prior to using the energy minimization program, mdrun, it may be convenient to combine these in a single job. This also makes it easy to ensure that the number of processors specified in the grompp call matches that used for mdrun.

Here is a batch job script, gromacs_glacier.pbs, for a job to run grompp, followed by mdrun. The script and data are located on Glacier in the directory /global/software/gromacs-3.3/job_examples/dppc_pme . To run the example, first copy the files from that directory to your own subdirectory. To submit the job to run on 4 processors, use:

Running grompp separately

Following is a script for running the GROMACS preprocessor, grompp, on the WestGrid Glacier cluster, glacier.westgrid.ca. The script accepts several arguments. The first argument is a run name, for example, "dppc", to be used as part of output file name and subsequently for the root of various file names associated with an mdrun job. The second argument is the number of processors to be used in the mdrun job, for example, 4. A final, optional, argument is a sequence number to be used as a suffix to the base run name. This is useful for simulations that are run as a series of jobs. The default sequence number is 1. Here is an example to show how the script can be run:

Submitting an mdrun job

After grompp has been run on the login node, a batch job can be submitted to run mdrun. If the TORQUE script shown below is called run_mdrun_glacier.pbs, it can be submitted to run on 4 processors (2 processors on each of 2 nodes) with:

Post-processing with tpbconv

Here is a script to run tpbconv, to process output from one mdrun job to prepare input for a subsequent job. It is presumed that the files from a previous run have names such as dppc.3.gro, dppc.3.trr, etc. formed from a base name (dppc in the example) and a sequence number (3). The job is submitted using a command of the form: